This project, entitled Molecular Mechanisms of Phytochrome Signaling (PI J. Clark Lagarias, UC Davis), focuses on gaining fundamental knowledge about the phytochrome family of protein light sensors. Phytochromes utilize linear tetrapyrroles (bilins) as chromophores to sense light quality, quantity and duration. Photochemical light sensing triggers conformational changes that modulate the behavior of living systems via target molecules that regulate downstream transcriptional cascades. The proposed investigations address the hypothesis that the fundamental mechanism of light sensing has remained conserved throughout billions of years of evolution since endosymbiotic capture of a cyanobacterium by a eukaryotic host. There are three specific aims focused on conservation of photoconversion and protein-chromophore interactions in plant and cyanobacterial phytochromes, the evolutionary genesis of plant phytochrome, and phytochrome photoconversion and signaling activity in land plants. By examining phytochromes from evolutionarily distant species ranging from cyanobacteria to plants, our studies seek to elucidate the basis of light sensing and the intramolecular structural changes that are used to control gene expression. Phytochromes from the glaucophyte Cyanophora paradoxa, the chlorophyte Micromonas pusilla, and the land plants Arabidopsis thaliana and Triticum aestivum (wheat), will be used to examine the hypothesis that light-regulated conformational change triggers translocation to the nucleus in all extant eukaryotic phytochromes. To test these hypotheses, we leverage computational analyses to guide experimental design, protein biochemistry and molecular biology to express and purify photoreceptors, enzymology and spectroscopy to understand light-induced changes in photoreceptor structure, and in vivo assessment of nuclear translocation and function in the model land plant Arabidopsis thaliana. Significance. Studies on phytochromes provide fundamental knowledge about how living systems regulate their behavior in response to the external environment. Phytochromes are key regulators for triggering seed germination, initiating early development of the seedling, and inducing flowering (sexual development). Because of their role in shade sensing, phytochromes are an important limiting factor for yield at high crop densities in modern agriculture. Application of the insights from our studies can improve nutrition, enhancing health, lengthening life, and reducing the burdens of illness and disability. Moreover, photosensory proteins are valuable tools for studying function and localization of mammalian proteins (optogenetics), and this work yields new tools for fundamental research into such systems.